GtSeqid2SeqnumMapping* gt_seqid2seqnum_mapping_new_seqcol(GtSeqCol *seqcol,
GtError *err)
{
GtSeqid2SeqnumMapping *mapping;
gt_error_check(err);
gt_assert(seqcol);
mapping = gt_malloc(sizeof *mapping);
mapping->filename = NULL;
mapping->map = gt_hashmap_new(GT_HASH_STRING, gt_free_func,
(GtFree) seqid_info_delete);
if (fill_mapping(mapping, NULL, seqcol, err)) {
gt_seqid2seqnum_mapping_delete(mapping);
return NULL;
}
mapping->cached_seqid = NULL;
return mapping;
}
void gt_region_mapping_delete(GtRegionMapping *rm)
{
if (!rm) return;
if (rm->reference_count) {
rm->reference_count--;
return;
}
gt_str_array_delete(rm->sequence_filenames);
gt_str_delete(rm->sequence_file);
gt_str_delete(rm->sequence_name);
gt_mapping_delete(rm->mapping);
gt_bioseq_delete(rm->bioseq);
gt_encseq_delete(rm->encseq);
gt_seq_col_delete(rm->seq_col);
gt_seqid2seqnum_mapping_delete(rm->seqid2seqnum_mapping);
gt_free(rm);
}
GtSeqid2SeqnumMapping* gt_seqid2seqnum_mapping_new_bioseq(GtBioseq *bioseq,
GtError *err)
{
GtSeqid2SeqnumMapping *mapping;
gt_error_check(err);
gt_assert(bioseq);
mapping = gt_malloc(sizeof *mapping);
mapping->filename = gt_cstr_dup(gt_bioseq_filename(bioseq));
mapping->map = gt_hashmap_new(GT_HASH_STRING, gt_free_func,
(GtFree) seqid_info_delete);
if (fill_mapping(mapping, bioseq, NULL, err)) {
gt_seqid2seqnum_mapping_delete(mapping);
return NULL;
}
mapping->cached_seqid = NULL;
return mapping;
}
static int update_seq_col_if_necessary(GtRegionMapping *rm, GtStr *seqid,
GtError *err)
{
int had_err = 0;
gt_error_check(err);
gt_assert(rm && seqid);
/* for mappings, we need to load the changed sequence, if needed... */
if (rm->mapping) {
if (!rm->sequence_file || (gt_str_cmp(rm->sequence_name, seqid))) {
gt_str_delete(rm->sequence_file);
/* ignore MD5 hashes when using region mappings */
if (gt_md5_seqid_has_prefix(gt_str_get(seqid))) {
rm->sequence_file = region_mapping_map(rm,
gt_str_get(seqid)
+GT_MD5_SEQID_TOTAL_LEN,
err);
} else
rm->sequence_file = region_mapping_map(rm, gt_str_get(seqid), err);
if (!rm->sequence_file)
had_err = -1;
else {
/* load new seqcol */
if (!rm->sequence_filenames)
rm->sequence_filenames = gt_str_array_new();
else
gt_str_array_reset(rm->sequence_filenames);
gt_str_array_add(rm->sequence_filenames, rm->sequence_file);
if (!rm->sequence_name)
rm->sequence_name = gt_str_new();
else
gt_str_reset(rm->sequence_name);
gt_str_append_str(rm->sequence_name, seqid);
gt_seq_col_delete(rm->seq_col);
rm->seq_col = gt_bioseq_col_new(rm->sequence_filenames, err);
if (!rm->seq_col)
had_err = -1;
}
}
} else {
/* ...otherwise, just make sure the seqcol is loaded */
if (!rm->seq_col) {
if (rm->encseq) {
if (!(rm->seq_col = gt_encseq_col_new(rm->encseq, err)))
had_err = -1;
} else {
gt_assert(rm->sequence_filenames);
if (!(rm->seq_col = gt_bioseq_col_new(rm->sequence_filenames, err)))
had_err = -1;
}
}
if (!had_err && rm->usedesc) {
if (rm->seqid2seqnum_mapping)
gt_seqid2seqnum_mapping_delete(rm->seqid2seqnum_mapping);
rm->seqid2seqnum_mapping =
gt_seqid2seqnum_mapping_new_seqcol(rm->seq_col, err);
if (!rm->seqid2seqnum_mapping) {
had_err = -1;
}
}
}
return had_err;
}
